Buggy code:
public abstract class KernelTransformFloat implements CoordinateTransform { protected int ndims ; protected float [ ] tmp ; protected float [ ] tmpDisplacement ; protected DenseMatrix64F gMatrix ; protected DenseMatrix64F dMatrix ; protected DenseMatrix64F wMatrix ; protected DenseMatrix64F lMatrix ; protected DenseMatrix64F yMatrix ; protected DenseMatrix64F I ; protected float [ ] [ ] aMatrix ; protected float [ ] bVector ; protected double stiffness = 0.0 ; protected boolean wMatrixComputeD = false ; protected boolean computeAffine = true ; protected boolean isInverse = false ; protected int nLandmarks ; protected float [ ] [ ] sourceLandmarks ; protected float [ ] [ ] targetLandmarks ; protected float [ ] weights ; protected float [ ] [ ] displacement ; KernelTransformFloat inv = null ; protected int initialContainerSize = 100 ; protected double increaseRaio = 0.25 ; protected int containerSize ; protected static Logger logger = LogManager . getLogger ( KernelTransformFloat . class . getName ( ) ) ; public KernelTransformFloat ( ) { } public KernelTransformFloat ( final int ndims ) { } public KernelTransformFloat ( final int ndims , final float [ ] [ ] srcPts , final float [ ] [ ] tgtPts ) { } public KernelTransformFloat ( final int ndims , final float [ ] [ ] srcPts , final float [ ] [ ] tgtPts , final float [ ] weights ) { } public KernelTransformFloat ( final float [ ] [ ] srcPts , final float [ ] [ ] aMatrix , final float [ ] bVector , final double [ ] dMatrixData ) { } public int getNumLandmarks ( ) { } public int getNumDims ( ) { } public float [ ] [ ] getSourceLandmarks ( ) { } public float [ ] [ ] getTargetLandmarks ( ) { } public float [ ] [ ] getAffine ( ) { } public float [ ] getTranslation ( ) { } public double [ ] getKnotWeights ( ) { } public void setLandmarks ( final float [ ] [ ] srcPts , final float [ ] [ ] tgtPts ) throws IllegalArgumentException { } public void updateSourceLandmark ( final int i , final float [ ] newSource ) { } public void updateTargetLandmark ( final int i , final float [ ] newTarget ) { } public void addMatch ( final double [ ] source , final double [ ] target ) { } public void addMatch ( final float [ ] source , final float [ ] target ) { } protected void expandLandmarkContainers ( ) { } private void setWeights ( final float [ ] weights ) { } public void setDoAffine ( final boolean estimateAffine ) { } private void initMatrices ( ) { } protected DenseMatrix64F computeReflexiveG ( ) { } protected void computeDeformationContribution ( final float [ ] thispt ) { } public void computeDeformationContribution ( final float [ ] thispt , final float [ ] result ) { } protected void computeD ( ) { } protected float normSqrd ( final float [ ] v ) { } public void solve ( ) { } public void solve ( final boolean isInverse ) { } public void computeW ( ) { } protected void computeL ( ) { } protected void computeP ( ) { } protected void computeK ( ) { } protected void computeY ( ) { } protected void reorganizeW ( ) { } public double [ ] transformPointAffine ( final double [ ] pt ) { } public void transform ( final float [ ] pt , final float [ ] result ) { } public float [ ] transformPoint ( final float [ ] pt ) { } public void transformInPlace ( final float [ ] pt ) { <START_BUG> computeDeformationContribution ( pt , tmp ) ; <END_BUG> for ( int i = 0 ; i < ( ndims ) ; ++ i ) { pt [ i ] = tmp [ i ] ; } } @ Override public float [ ] apply ( final float [ ] location ) { } @ Override public void applyInPlace ( final float [ ] location ) { } protected void srcPtDisplacement ( final int i , final int j , final float [ ] res ) { } protected void srcPtDisplacement ( final int i , final float [ ] pt , final float [ ] res ) { } public abstract void computeG ( float [ ] pt , DenseMatrix64F mtx ) { } }

Fix:
transform ( pt , tmp ) ;